


Experimental

by MarvelFan_hkf



Category: Marvel Cinematic Universe, Spider-Man (Tom Holland Movies), The Avengers (Marvel Movies), spider-man homecoming
Genre: Avenger Kidnapped, Avengers Family, Avengers Protecting Peter Parker, Gen, HYDRA is a bunch of assholes, Help Peter Parker, Human Experimentation, Hurt Peter Parker, Hydra Peter Parker, Kidnapped, Peter Parker Needs a Hug, Peter Parker almost dies, Peter Parker is a Mess, Protective Steve Rogers, Protective Tony Stark, Tony Stark Acting as Peter Parker's Parental Figure, Tony Stark Needs a Hug
Language: English
Status: In-Progress
Published: 2019-07-02
Updated: 2020-03-05
Packaged: 2020-06-02 23:19:11
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 5
Words: 2,946
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19451542
Author URL: https://archiveofourown.org/users/MarvelFan_hkf/pseuds/MarvelFan_hkf
Summary: It started out as just a normal mission. The Avengers had received a call about an abandoned HYDRA base and had decided to go check it out. It was supposed to be a quick and easy trip, but Tony had still been hesitant about letting Peter come. Yes, the boy was Spiderman, but Tony couldn’t help wanting to look out for the kid he considered his son. Alas, after what seemed like hours of Peter’s relentless begging, Tony decided to let him tag along.--------------(The Avengers get taken by hydra and are forced to watch Peter Parker get tortured and experimented on)





	1. Give in To the Darkness

**Author's Note:**

> I DO NOT OWN ANY OF THE CHARACTERS IN THIS STORY
> 
> Hello everyone! I am super excited about this story, and can't wait to see where it leads! 
> 
> If you haven't read my other story, go check it out!  
> Its called, "Spider On The Run" 
> 
> Please leave comments down below of any suggestions about this story, and anything you want to see in upcoming chapters. 
> 
> Thank you, and Hope You Enjoy!!

It started out as just a normal mission. The Avengers had received a call about an abandoned HYDRA base and had decided to go check it out. It was supposed to be a quick and easy trip, but Tony had still been hesitant about letting Peter come. Yes, the boy was Spiderman, but Tony couldn’t help wanting to look out for the kid he considered his son. Alas, after what seemed like hours of Peter’s relentless begging, Tony decided to let him tag along. 

Peter was beyond excited. This was his first REAL mission with all the Avengers. Yes, he had been on smaller missions with only one or two of them at a time, but now he was going on a big mission with the WHOLE team! He could hardly contain his excitement. 

Steve should have known that something was wrong when the base seemed so clean. Normally abandoned bases were covered in dust and filth. This one seemed to still be in perfect condition. Steve tried to ignore the gut feeling that was telling him something wasn’t right. As much as he tried, he still clutched his shield a little tighter than usual. 

Natasha had the same gut feeling as Steve. The floors were still relatively clean, the glass walls were still clear, and the air wasn’t as dusty as other abandoned bases they had explored. She couldn’t help but feel like something terrible was going to happen. 

Tony felt the same way. He thought it was strange that the base had been so clean, but that didn’t bother him as much as the fact that the security cameras were still up and running. 

“Why would an abandoned base still have the cameras on?” Tony thought to himself as he entered the room with the monitors to the cams. They showed every hallway, every door, and every cell in the place. Tony looked at the cams to what seemed like surgical rooms and was taken aback by the fact that he could see what looked like dried blood on the floors and walls of each room. The sight sent a shiver down his spine. He left the room quickly, wanting to finish the mission as fast as possible. 

Peter’s spidey senses had been going off ever since they entered the base. However, he had been too distracted by his excitement to notice. The team had decided to split up and look around, and now that he was alone, he could feel his senses speaking to him. The communication device would buzz occasionally in his ear, as someone would say that they hadn’t found anything. 

Peter turned down an especially dark hallway, and his senses started to scream at him. 

Danger, Danger, Danger…

He could barely think over the voice in his head. He was shaking from the shiver sent down his spine. 

DANGER, DANGER, DANGER…..

His knees crumpled underneath him and he fell to the floor. Peter became aware of the sound of footsteps coming towards him, but he was too overwhelmed to do anything. 

DANGER, RUN, DANGER…….

He felt hands yanked him off the floor. He tried desperately to fight but found himself suddenly weak as a prick was felt in his neck. 

RUn, Run, run……..

His senses didn’t stop screaming until he was overcome by a wave of darkness. 

\---------------------------------------------------------------------

Tony entered the strange looking room with caution. This room was smaller than the others and had no windows. The walls were white, the floor was white, and even the ceiling was white. He got a strange feeling when he entered the room…… Like something was about to happen. 

His thoughts were confirmed when he heard the door close and lock behind him. 

Tony immediately ran to the door and started to bang as hard as he could on it. He screamed into his comms for someone to help him. 

He then became aware of the gas that had started filling the room through a small vent in the floor. 

He screamed louder. Nobody answered. He was starting to feel dizzy as the gas reached his nose. His head was throbbing and he dropped to the floor as his strength was drained. He felt himself drifting off into sleep when one last thought entered his head. 

Peter…..

The darkness consumed him as he fell into a deep sleep. 

\------------------------------------------------------------------------------

Steve ran as fast as he could when he heard Tony yelling through the comms. 

He turned countless corners but kept getting lost amongst the maze of mase. He suddenly became aware of the running footsteps coming after him and ran even faster. His team was in trouble. 

Steve began calling for Natasha, Bruce, and all the other team members to get to safety. No one answered him. 

Steve felt a sharp prick in his neck, and it was as if all his strength was drained. He dropped to the ground in exhaustion, as the footsteps caught up to him. He felt he dragged away as the darkness consumed him. 

\--------------------------------------------------------------------------------


	2. Waking up

**Summary for the Chapter:**

> “Hello?” He said loudly. Hoping someone would hear him. He waited a few moments and started feeling discouraged when there was no response. 
> 
> “Is anyone there?” He yelled again. A few more moments passed before he heard….
> 
> “Tony?” A familiar voice asked from nearby.

**Notes for the Chapter:**

> I DO NOT OWN ANY OF THE CHARACTERS IN THIS STORY. 
> 
> Hey guys! Don't worry, I'm still alive. Sorry for the insanely long time it took me to update this! I worked at a summer camp and the past month has been CRAZY busy. 
> 
> I PINKY PROMISE that will not happen again! I plan on having the next chapter released soon!! 
> 
> More notes at the end!

Tony opened his eyes, only to find that it was just as dark as when his eyes were closed. A feeling of fear washed over him as he began to remember the events that had led up to the situation he currently found himself in. 

“Hello?” He said loudly. Hoping someone would hear him. He waited a few moments and started feeling discouraged when there was no response. 

“Is anyone there?” He yelled again. A few more moments passed before he heard….

“Tony?” A familiar voice asked from nearby. 

“Steve?!” Tony asked excitedly. “Oh thank god you’re here.” 

“Tony, where are the others,” Steve responded. His voice was laced with a hint of worry. 

“Well maybe we could find out if they turned these damn lights on,” Tony responded sarcastically. 

As if on cue, the room was suddenly filled with a blinding light. Tony instinctively tried to raise his hands to his face to shield his eyes but had no luck since his hands were bound to the chair he was sitting in. 

It took a few minutes for his eyes to adjust. When they finally did, Tony took a good look at his surroundings. He was sitting in an all-white room, (White floors, white ceilings, white walls, white door……) surrounded by some of the other Avengers. They were bound to their chairs, (which were arranged in a line across the width of the room) and they were all unconscious. That is, all but Tony and Steve. 

Tony sat in the middle of the room. Steve sat to his right and Natasha on his left. Bucky sat on the other side of Steve, and Rhodey on the other side of Natasha. 

The other heroes were starting to wake up due to the sudden change in lighting. Bucky was the first to start talking. 

“So does anyone want to tell me what the fuck is going on,” Bucky asked aggressively. 

The sound of static suddenly filled the room, as a voice came through what sounded like an intercom. 

“I see that you all have finally decided to wake up,” A deep voice boomed through the speakers. The voice sent chills down Tony’s spine. 

“What the do you want from us,” Steve yelled at the voice.

“Oh… I'm surprised you haven’t already noticed,” The booming voice continued.

“Haven’t noticed what?” Tony yelled. He was getting tired of this. 

“I have already taken what I need.” The voice said, laughing slightly at the end. 

The realization hit Tony like a train. All the AAvengers that came on the mission were sitting in this room……………….. All but one. Tony was overflowing with rage

“WHERE THE FUCK IS HE,” Tony screamed at the voice. The others looked at him with confusion for a few moments before coming to the same realization. 

The voice laughed. It was evil. The laughter sounded like an evil villain from a movie. 

“Ahh…...don’t worry, I haven’t hurt him………yet,” The voice said. The room was filled with static as the intercom was turned off. 

Tony was furious. He swore to himself that he would kill anyone who laid a hand on the kid. 

There was a loud buzzing sound as the wall in front of him lowered to reveal a large window into another all-white room. In the middle of the room, there was a single chair. Sitting in the chair was a small figure with curly brown hair that Tony would recognize anywhere. 

“Peter,” Tony whispered as he stared at the unconscious boy.

**Notes for the Chapter:**

> Short chapter! really just setting up for what is going to happen next. The next few chapters should have some good action in them so just hang tight! 
> 
> Please leave a comment! I absolutely LOVE reading what you guys comment! Feel free to comment on any advice, tips, or even ideas you have for this story, and where it is going to go. Also, feel free to leave any prompt or story ideas in the comments! The idea for this story actually came from a comment someone left on my other work (Which you should go check out lol)! 
> 
> Thank you to everyone who has read this story! I can't wait to keep going!


	3. The Boy In The Chair

**Summary for the Chapter:**

> Peter continued to take in his surroundings when he heard a small whisper…..
> 
> “Peter,”
> 
> or:  
> Peter wakes up and starts to wish he hadn't.

**Notes for the Chapter:**

> I DO NOT OWN ANY OF THE CHARACTERS IN THIS STORY!
> 
> New chapter!! Sorry for the long wait. School is starting for me, so I'm going to try to keep updating as fast as I can, but I apologize in advance if any updates take longer than usual. 
> 
> PLEASE LEAVE COMMENTS!  
> I love reading all of you guys' comments, and they really help me stay motivated to keep working on this story!  
> Also, feel free to leave any ideas or prompts for other stories in the comments! The idea for this story was actually from a comment on my other work, so do not hesitate to tell me what you would like to see! 
> 
> Thank you to everyone who has read this so far! I really hope you enjoy this story!

Peter’s eyes fluttered open briefly before snapping shut again due to the blinding light they were met with. When he opened his eyes again, he did not recognize his surroundings. He was sitting in the middle of a small, all-white room. In the corner of the room, there was a small, metal table with a tray of scary-looking tools on it. Peter continued to take in his surroundings when he heard a small whisper…..

“Peter,”

He snapped his head to where the sound came from and saw that the wall in front of him was made entirely out of glass. He quickly found the source of the whisper. Sitting directly in front of him was Tony. The expression on his face was one of pure anger and fear.  
Peter knew that the only reason he had been able to hear Tony was due to his enhanced senses. Nevertheless, he tried to talk back to the man. 

“Tony,” the boy whispered back. He knew the man didn’t hear him, but he must have read his lips because his eyes widened at the gesture. 

Suddenly, a loud static noise filled the room. Peter attempted to bring his hands up to his ears to block out the horrible noise but quickly found that he was bound to the chair by strong metal cuffs. 

The static ended and a deep voice replaced it. 

“I’m glad to see you are awake, little spider,” Peter cringed at the nickname, only Natasha was allowed to call him that. 

“I hope you are ready. Today is a big day for you,” The voice continued. 

“DON’T YOU FUCKING TOUCH HIM,” Tony screamed with such volume it caused Peter to flinch. The man was furious and terrified. Tony’s fear only made Peter even more afraid of what was to come. 

“Oh I’m not going to touch him, but they will,” The voice replied as a hidden door in his room opened. Two men dressed in all white walked into the room and went over to the table in the corner. One grabbed a syringe full of a strange substance, while the other grabbed a large pair of headphones. Peter flinched as he felt a pinch in his neck, and one of the men forcefully put the headphones over his ears. 

“We are going to start with a quick test of your senses, starting with hearing,” The voice came back over the speakers. 

Suddenly, Peter’s ears were filled with a terrible pulsing tone. The noise was so loud it felt like his brain was shaking in his skull. His ears burned, his head throbbed. Peter had never felt pain like this before. The pulse got louder with each passing second. Black dots filled his vision as his body threatened unconsciousness. Peter became aware of the fact that he was screaming. After what felt like hours of brutal torture, one of the men took off the headphones. Peter slumped forward and felt the warm liquid trickle out of his ears and down his face. He couldn’t hear anything. His head still throbbed. 

Peter forced himself to look up and could see the horrified faces of the Avengers on the other side of the window. Tony’s face had gone white as a sheet, and while Peter couldn’t hear it, he could see that the man was screaming furiously at the air. 

Peter made eye contact once again with Tony before he was engulfed by familiar darkness.


	4. Don't Touch Him

**Summary for the Chapter:**

> (the same as chapter 3 but from Tony's POV)

**Notes for the Chapter:**

> I DO NOT OWN ANY OF THE CHARACTERS IN THIS STORY
> 
> Yay, this update didn't take a whole week! I am working on the next chapter now so it should be up soon. 
> 
> Thank you to everyone who has left kudos or commented on this story! I really appreciate it!

“Peter.” 

The boy’s eyes fluttered open, only to be snapped shut again. Tony knew the lights must be too bright for Peter’s enhanced senses. When they first met, Peter had told Tony that his senses were “dialed to 11.” The lights were already blinding for Tony, so he could only imagine how bad they were for Peter. All he wanted to do was hug the boy and tell him it would be alright. 

Peter’s eyes slowly opened again, and Tony watched as the boy started to take in his surroundings. He looked at each wall with a confused expression but still hadn’t noticed the window in front of him. 

“Peter,” Tony whispered a little louder this time. He could hardly contain his relief to see the boy awake. 

Peter’s head whipped around as soon as Tony had spoken. The boy looked confused and terrified. As soon as they made eye contact, Tony was filled with rage and terror. The childlike innocence in Peter’s eyes was replaced with fear. Tony hated seeing the kid like this and swore to kill anyone who laid a finger on him. 

The eye contact only broke when a loud static noise filled the room. Tony could see the boy flinch and try to raise his hands to his ears, only to find they were bound to the chair. Peter cringed at the volume of the noise, and Tony continued to get angrier.

The static stopped, and Tony heard the horrifyingly familiar voice come over the speakers. 

“I’m glad to see you are awake, little spider,” The voice said. 

“Don’t you dare hurt him,” Tony thought to himself as the man spoke. 

“I hope you are ready. Today is a big day for you,” the voice continued. Tony could no longer hold back his rage. 

“DON’T YOU FUCKING TOUCH HIM,” Tony screamed at the speakers. The other Avengers ( who had been sitting and quietly observing the whole time ) all turned to face him. They had not expected this level of rage from Tony. They knew he cared for the boy but didn’t know the extent. Peter whipped his head around to face the man again, the fear in his eyes only growing. 

“Oh I’m not going to touch him, but they will,” The voice continued as a door in Peter’s room opened and two men in all white walked in. Tony was terrified. He looked around to see that all the others had the same fearful look in their eyes as they watched what was happening. Tony turned back to the boy just in time to see him flinch as a needle was jabbed into his neck. A large pair of headphones was forcefully shoved over the boy’s ears. 

“We are going to start with a test of your senses, starting with hearing,” as soon as the voice said it, Tony knew what was about to happen. 

Tony watched as Peter’s eyes suddenly widened and his limbs tensed up. The boy started shaking violently as his face curled into a pain-filled expression. Tony could see blood where Peter was clenching his fists too tight. It was absolute torture to watch. 

Just when Tony thought it couldn’t get any worse, Peter started screaming. A blood-curdling scream came from the boy as he continued to seize from the pain. Tony could feel himself on the verge of a panic attack as the kid, he loved was tortured in front of his very eyes. 

After what felt like forever, one of the men stepped back into the room and roughly removed the headphones from the boy’s ears. Tony could see blood running from the boy’s ears and down his face. 

Tony had never been angrier in his life.

“HOW DARE YOU FUCKING HURT HIM HE’S A FUCKING KID,” He screamed. Tony loved the kid like he was his own, and now he was watching him be tortured. He continued to scream profanities at the air until his throat felt raw. When he looked back at the window, Peter had passed out again. 

Tony stared at the boy. His familiar brown curls were soaked with sweat. His eyes, usually full of happiness, were shut. Tony held back tears as he whispered...

“I’m sorry Pete. I’m so so sorry,"

**Notes for the Chapter:**

> Please leave a comment! You guy's comments really help keep me motivated to continue! 
> 
> Also, feel free to leave any ideas for other stories to write when I'm done with this one! I want to know what you guys want to see from me!
> 
> Thank you!


	5. Update

**Summary for the Chapter:**

> Update on why I haven't been posting

Hello everyone. 

As you guys can see it has been a very long time since I have posted.

I want to apologize for my inactivity and offer an explanation for you guys. 

I had every intention of continuing this story. I had planned and outlined at least 5 more chapters and didn't plan on stopping there. When the school year started, my mental health started to decline. I was dealing with a lot of stress, anxiety, and many other things. In October my mental health and stability took a nosedive. I was always anxious and cried almost every day. I felt depressed and worthless. I felt unwanted and unloved. December was the worst of it all. My self-worth hit rock bottom, and I started having very bad thoughts. I was scared of my own mind. When the new year started, I decided that I needed to change. I have since then worked very hard on my mental health and am happy to say that I am out of the scary place I was in. I still have bad days and am nowhere near perfect or happy, but with the help of friends and the people around me, I am improving. 

All that being said, I am sorry about not continuing this story. I am currently working on a new story idea and can't wait to start writing again. 

Thank you everyone who read this story and left a comment or Kudos. You guys are what inspires me to continue.


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